diff options
Diffstat (limited to 'scripts/fastq2fasta.scm')
| -rw-r--r-- | scripts/fastq2fasta.scm | 8 |
1 files changed, 2 insertions, 6 deletions
diff --git a/scripts/fastq2fasta.scm b/scripts/fastq2fasta.scm index ef4682c..6fa985c 100644 --- a/scripts/fastq2fasta.scm +++ b/scripts/fastq2fasta.scm @@ -12,7 +12,6 @@ (define ref-fasta (input "ref_fasta" - #:type 'File #:other '((secondary-files . #(".amb" ".ann" ".bwt" ".pac" ".sa"))))) (define output-sam @@ -23,7 +22,6 @@ (define fastq-forward (input "fastq_forward" - #:type 'File #:label "input fastq file to map (single-end or forward for pair-end)")) (define fastq-reverse @@ -58,7 +56,7 @@ #:type 'File #:source "bcftools_norm/stdout"))) (command "bcftools_index_after_normalization" - (list "bcftools" "index" (input "normalized" #:type 'File)) + (list "bcftools" "index" (input "normalized")) #:outputs (list (output "index_after_normalization" #:type 'File #:binding '((glob . "$(inputs.normalized.basename)")) @@ -70,12 +68,11 @@ "-i" "'QUAL > 10 && GT=\"a\"'" "-Oz" "--threads" threads (input "index_after_normalization" - #:type 'File #:other '((secondary-files . #(".csi"))))) #:outputs (list (output "bcftools_view_qc_output_vcf" #:type 'stdout)) #:other '((stdout . "bcftools_view_output.vcf.gz"))) (command "bcftools_index_after_qc" - (list "bcftools" "index" (input "bcftools_view_qc_output_vcf" #:type 'File)) + (list "bcftools" "index" (input "bcftools_view_qc_output_vcf")) #:outputs (list (output "index_after_qc" #:type 'File #:binding '((glob . "$(inputs.bcftools_view_qc_output_vcf.basename)")) @@ -88,7 +85,6 @@ "-i" "'QUAL > 10 && GT=\"a\"'" "-Hla" "-f" ref-fasta (input "index_after_qc" - #:type 'File #:other '((secondary-files . #(".csi")))))) (command "set_sample_id" (list "sed" "s/^>.*/>$(inputs.sample_id)/g") |